Question: What is a "star index" tool dependency?
0
gravatar for bisht20diksha
3 months ago by
INDIA
bisht20diksha10 wrote:

hi- i want to work with rMATS tool that require star indexes. Can anyone please explain me what are these star indexes? As i am unable to understand it properly.

mats rna-seq rna star • 138 views
ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson24k • written 3 months ago by bisht20diksha10
0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

The star indexes are associated with the tool RNA STAR and are a requirement/dependency for rMATS.

The rMATS tool is not wrapped for Galaxy (at least in the Main Tool Shed http://usegalaxy.org/toolshed). So, I am assuming that you are running this line command.

For help with install, config, and usage, please see the support resources at that tool's development site: http://rnaseq-mats.sourceforge.net/. Or, consider a general bioinformatics forum such as: https://www.biostars.org/.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson24k

okay. Can we generate star indexes for our genome using RNA STAR at galaxy?

ADD REPLYlink written 3 months ago by bisht20diksha10

Indexes can be generated using the RNA STAR Data Manager in your own Galaxy (not on the public servers). These will be linked to the RNA STAR tool, and not others. Even though I don't see why these indexes couldn't be used command-line with other tools, it is the long way to go about generating the data given that the target tool will not be used within Galaxy (rMATS). But you can decide. Thanks! Jen

ADD REPLYlink written 3 months ago by Jennifer Hillman Jackson24k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 143 users visited in the last hour